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This page was generated on 2021-05-06 12:34:16 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the ALDEx2 package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 42/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ALDEx2 1.22.0 (landing page) Greg Gloor
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ALDEx2 |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ALDEx2_1.22.0.tar.gz |
StartedAt: 2021-05-05 23:07:36 -0400 (Wed, 05 May 2021) |
EndedAt: 2021-05-05 23:13:32 -0400 (Wed, 05 May 2021) |
EllapsedTime: 356.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ALDEx2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ALDEx2_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ALDEx2.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ALDEx2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ALDEx2’ version ‘1.22.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ALDEx2’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed aldex.corr 116.809 4.045 121.411 aldex.glm.effect 6.651 0.028 6.684 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
ALDEx2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ALDEx2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘ALDEx2’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ALDEx2)
ALDEx2.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(ALDEx2) Loading required package: zCompositions Loading required package: MASS Loading required package: NADA Loading required package: survival Attaching package: 'NADA' The following object is masked from 'package:stats': cor Loading required package: truncnorm > > test_check("ALDEx2") [ FAIL 0 | WARN 4 | SKIP 0 | PASS 22 ] > > proc.time() user system elapsed 53.435 1.336 54.833
ALDEx2.Rcheck/ALDEx2-Ex.timings
name | user | system | elapsed | |
ALDEx2m-package | 0 | 0 | 0 | |
aldex | 2.277 | 0.464 | 2.744 | |
aldex.clr-class | 0.074 | 0.006 | 0.080 | |
aldex.clr.function-methods | 0.077 | 0.005 | 0.082 | |
aldex.corr | 116.809 | 4.045 | 121.411 | |
aldex.effect | 3.459 | 0.013 | 3.475 | |
aldex.glm | 1.315 | 0.017 | 1.333 | |
aldex.glm.effect | 6.651 | 0.028 | 6.684 | |
aldex.kw | 2.090 | 0.009 | 2.100 | |
aldex.plotFeature | 0.099 | 0.003 | 0.103 | |
aldex.set.mode | 0.054 | 0.003 | 0.057 | |
aldex.ttest | 0.149 | 0.004 | 0.153 | |
expectedDistance | 0.360 | 0.021 | 0.381 | |
getDenom-method | 0.097 | 0.005 | 0.102 | |
getFeatureNames-method | 0.055 | 0.002 | 0.056 | |
getFeatures-method | 0.055 | 0.002 | 0.056 | |
getMonteCarloInstances-method | 0.055 | 0.001 | 0.057 | |
getMonteCarloReplicate-method | 0.054 | 0.001 | 0.056 | |
getMonteCarloSample-method | 0.055 | 0.001 | 0.057 | |
getReads-method | 0.055 | 0.002 | 0.057 | |
getSampleIDs-method | 0.062 | 0.006 | 0.068 | |
numConditions-method | 0.055 | 0.002 | 0.056 | |
numFeatures-method | 0.055 | 0.003 | 0.058 | |
numMCInstances-method | 0.055 | 0.003 | 0.058 | |
plot.aldex | 0 | 0 | 0 | |